[2024-01-24 12:22:48,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference
[2024-01-24 12:22:49,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,793] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cdfac53-b522-4147-b6c7-5474c64becfc/GCF_015694525.1_ASM1569452v1_genomic.fna.gz | prodigal -d GCF_015694525.1_ASM1569452v1_genomic.fna/cds.fna -a GCF_015694525.1_ASM1569452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:29,426] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:29,427] [INFO] Task started: HMMsearch
[2024-01-24 12:23:29,427] [INFO] Running command: hmmsearch --tblout GCF_015694525.1_ASM1569452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference/reference_markers.hmm GCF_015694525.1_ASM1569452v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:29,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:29,738] [INFO] Found 6/6 markers.
[2024-01-24 12:23:29,798] [INFO] Query marker FASTA was written to GCF_015694525.1_ASM1569452v1_genomic.fna/markers.fasta
[2024-01-24 12:23:29,799] [INFO] Task started: Blastn
[2024-01-24 12:23:29,799] [INFO] Running command: blastn -query GCF_015694525.1_ASM1569452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference/reference_markers.fasta -out GCF_015694525.1_ASM1569452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:30,453] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:30,459] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:30,460] [INFO] Target genome list was writen to GCF_015694525.1_ASM1569452v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:30,465] [INFO] Task started: fastANI
[2024-01-24 12:23:30,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cdfac53-b522-4147-b6c7-5474c64becfc/GCF_015694525.1_ASM1569452v1_genomic.fna.gz --refList GCF_015694525.1_ASM1569452v1_genomic.fna/target_genomes.txt --output GCF_015694525.1_ASM1569452v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:50,678] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:50,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:50,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:50,696] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:50,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:50,696] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	100.0	1970	1972	95	conclusive
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	88.0101	1372	1972	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	85.9201	1412	1972	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	85.0772	1283	1972	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	84.6297	1293	1972	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	84.5122	1210	1972	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	84.0792	1099	1972	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	83.6687	1033	1972	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	83.5858	993	1972	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	82.8755	1110	1972	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.7193	989	1972	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.1932	752	1972	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.1485	764	1972	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	74.8969	50	1972	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	74.8753	62	1972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:50,698] [INFO] DFAST Taxonomy check result was written to GCF_015694525.1_ASM1569452v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:50,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:50,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:50,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference/checkm_data
[2024-01-24 12:23:50,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:50,755] [INFO] Task started: CheckM
[2024-01-24 12:23:50,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015694525.1_ASM1569452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015694525.1_ASM1569452v1_genomic.fna/checkm_input GCF_015694525.1_ASM1569452v1_genomic.fna/checkm_result
[2024-01-24 12:25:24,508] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:24,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:24,532] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:24,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:24,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015694525.1_ASM1569452v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:24,533] [INFO] Task started: Blastn
[2024-01-24 12:25:24,534] [INFO] Running command: blastn -query GCF_015694525.1_ASM1569452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1438c75a-4e63-4651-9721-6ad9f43c5e0d/dqc_reference/reference_markers_gtdb.fasta -out GCF_015694525.1_ASM1569452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:25,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:25,484] [INFO] Selected 16 target genomes.
[2024-01-24 12:25:25,484] [INFO] Target genome list was writen to GCF_015694525.1_ASM1569452v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:25,496] [INFO] Task started: fastANI
[2024-01-24 12:25:25,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cdfac53-b522-4147-b6c7-5474c64becfc/GCF_015694525.1_ASM1569452v1_genomic.fna.gz --refList GCF_015694525.1_ASM1569452v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015694525.1_ASM1569452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:47,660] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:47,673] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:47,674] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_015694525.1	s__Hymenobacter ruricola	100.0	1970	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016427455.1	s__Hymenobacter sp016427455	87.8462	1412	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_015694735.1	s__Hymenobacter properus	85.9394	1409	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016734815.1	s__Hymenobacter rubidus	85.0593	1285	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056375.1	s__Hymenobacter negativus_A	84.8178	1272	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_012275535.1	s__Hymenobacter artigasi	84.4637	1216	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967845.1	s__Hymenobacter sp018967845	84.1614	1131	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_001507645.1	s__Hymenobacter sedentarius	84.0487	1103	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816145.1	s__Hymenobacter lapidarius	83.6897	1029	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	83.5947	992	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640435.1	s__Hymenobacter frigidus	83.3381	1054	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571495.1	s__Hymenobacter negativus	83.1035	1334	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	82.8768	1110	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972495.1	s__Hymenobacter terrenus	82.0057	1049	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	79.4351	754	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204745.1	s__Hymenobacter amundsenii	78.831	721	1972	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:47,676] [INFO] GTDB search result was written to GCF_015694525.1_ASM1569452v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:47,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:47,680] [INFO] DFAST_QC result json was written to GCF_015694525.1_ASM1569452v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:47,680] [INFO] DFAST_QC completed!
[2024-01-24 12:25:47,680] [INFO] Total running time: 0h2m59s